--- a/lexmapr/definitions.py	Wed Aug 31 14:32:14 2022 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,210 +0,0 @@
-"""Static definitions"""
-
-import os
-
-
-# root path
-ROOT = os.path.dirname(__file__)
-
-# URL to list of OLS ontologies where download link is given
-embl_ontologies = 'https://www.ebi.ac.uk/ols/ontologies'
-
-# beginning of URL to ontology PURL
-purl_link = 'http://purl.obolibrary.org/obo/'
-
-# directory for downloaded OWL files
-owl_dir = 'lexmapr/owl_files'
-
-# path to database with synonyms from predefined resources and from OWL files
-synonym_db = 'lexmapr/owl_files/label_synonyms.db'
-
-# path to database with all ontologies of interest
-ontol_db = 'lexmapr/owl_files/ontol_table.db'
-
-
-# ontologies of interest
-ontol_interest = [#'BFO',
-                  #'CHEBI',
-                  #'ENVO',
-                  'FOODON',
-                  #'GENEPIO',
-                  'NCBITAXON', # NCBITaxon is not valid as of April 2022
-                  #'OGMS',
-                  #'PATO',
-                  #'PCO',
-                  #'UBERON',
-                 ]
-
-# ontology accessions that do not have labels or are placeholders as of April 2022
-# will skip in database building
-missing_ontol_labels = ['GENEPIO_0001367','GENEPIO_0001368','GENEPIO_0001369','GENEPIO_0001370',
-                        'GENEPIO_0001372','GENEPIO_0001373','_MIAA_0000021',
-                       ]
-
-# terms indicating that the metadata was not given/collected; will output empty results
-not_provided = ['not applicable','unknown','n a','not provided','not available','miscellaneous',
-                'not collected','missing','unidentified','unknown','none','unamed','other',
-                'undetermined','not known','no history given','no source specified','null',
-                'unspecified','not reported','not available not collected','not isolated',
-                'not available','not provided','xxx','mising','misng','other','unidentified',
-                'not determined other','reported later','intact unknown','not determined',
-                'not ascertained','unk','nd','nd others','nd other','etc','na','',' ',
-                'not supplied','not specified',
-               ]
-
-# below are bin definitions
-# TODO: food consumer group:FOODON_03510136 changed, formatted as '* as food consumer'
-#       can collect as 'for *' in text?
-#fo_consumer = []
-
-fo_product = ['algal food product:FOODON_00001184',
-              'amphibian:FOODON_03411624',
-              'amphibian or reptile food product:FOODON_00002200',
-              'animal based refined or partially-refined food product:FOODON_00001595',
-              'avian egg food product:FOODON_00001105',
-              'avian food product:FOODON_001251',
-              'bakery food product:FOODON_00001626',
-              'cell-based technology food product:FOODON_00003376',
-              'dairy food product:FOODON_00001256',
-              'dietary supplement:FOODON_03401298',
-              'fish egg food product:FOODON_00001250',
-              'fish food product:FOODON_00001248',
-              'food product analog:FOODON_00001871',
-              'food product component:FOODON_00001714',
-              'fungus food product:FOODON_00001143',
-              'game animal food product:FOODON_00002477',
-              'insect food product:FOODON_00001177',
-              'meat food product:FOODON_00002477',
-              'microbial food product:FOODON_00001145',
-              'plant food product:FOODON_00001015',
-              'poultry food product:FOODON_00001283',
-              'prepared food product:FOODON_00001180',
-              'processed food product:FOODON_03311737',
-              'reptile egg food product:FOODON_00002199',
-              'seafood product:FOODON_00001046',
-              'shellfish food product:FOODON_00001293',
-              'soup food product:FOODON_00002257',
-              'sustainable agriculture food product:FOODON_00003375',
-              'vegetarian food product:FOODON_00003194',
-              'vertebrate animal food product:FOODON_00001092',
-             ]
-
-fo_quality = ['food (acidified):FOODON_03301625',
-              'food (adulterated):FOODON_00003367',
-              'food (baked):FOODON_00002456',
-              'food (batter-coated):FOODON_00002662',
-              'food (blanched):FOODON_00002767',
-              'food (blend):FOODON_00003889',
-              'food (boiled):FOODON_00002688',
-              'food (breaded):FOODON_00002661',
-              'food (broiled or grilled):FOODON_00002647',
-              'food (canned):FOODON_00002418',
-              'food (chilled):FOODON_00002642',
-              'food (chopped):FOODON_00002777',
-              'food (cleaned):FOODON_00002708',
-              'food (colored):FOODON_00002650',
-              'food (comminuted):FOODON_00002754',
-              'food (cooked):FOODON_00001181',
-              'food (deep-fried):FOODON_03307052',
-              'food (dehydrated):FOODON_00002643',
-              'food (dried):FOODON_03307539',
-              'food (fat or oil coated):FOODON_03460233',
-              'food (fermented):FOODON_00001258',
-              'food (filled):FOODON_00002644',
-              'food (flavored):FOODON_00002646',
-              'food (freeze-dried):FOODON_03301752',
-              'food (fresh):FOODON_00002457',
-              'food (fried):FOODON_00002660',
-              'food (frozen):FOODON_03302148',
-              'food (genetically-modified):FOODON_03530251',
-              'food (ground):FOODON_00002713',
-              'food (harvested):FOODON_00003398',
-              'food (heat treated):FOODON_03316043',
-              'food (hulled):FOODON_00002720',
-              'food (hydrolized):FOODON_00002653',
-              'food (irradiated):FOODON_03305364',
-              'food (juiced):FOODON_00003499',
-              'food (liquid):FOODON_03430130',
-              'food (milled):FOODON_00002649',
-              'food (not genetically-modified):FOODON_00003379',
-              'food (organically grown):FOODON_03306690',
-              'food (packaged):FOODON_00002739',
-              'food (packed in high pressurised containers):FOODON_03317139',
-              'food (pan-fried):FOODON_00002463',
-              'food (paste):FOODON_00003887',
-              'food (pasteurized):FOODON_00002654',
-              'food (peeled):FOODON_00002655',
-              'food (pickled):FOODON_00001079',
-              'food (powdered):FOODON_00002976',
-              'food (precooked):FOODON_00002971',
-              'food (precooked, frozen):FOODON_03305323',
-              'food (preserved):FOODON_00002158',
-              'food (puffed):FOODON_00002656',
-              'food (raw):FOODON_03311126',
-              'food (rehydrated):FOODON_00002755',
-              'food (roasted):FOODON_00002744',
-              'food (salted):FOODON_03460173',
-              'food (seasoned):FOODON_00002733',
-              'fruit (seedless):FOODON_00003461',
-              'food (semiliquid):FOODON_03430103',
-              'food (semisolid):FOODON_03430144',
-              'food (sliced):FOODON_00002455',
-              'food (smoked or smoke-flavored):FOODON_03460172',
-              'food (solid):FOODON_03430151',
-              'food (spoiled):FOODON_00003366',
-              'food (starch or flour thickened):FOODON_03315268',
-              'food (steamed):FOODON_00002657',
-              'food (sugar-free):FOODON_03315838',
-              'food (textured):FOODON_00002658',
-              'food (toasted):FOODON_00002659',
-              'food (unprocessed):FOODON_03316056',
-              'food (unstandardized):FOODON_03315636',
-             ]
-
-fo_organism = ['algae:FOODON_03411301',
-               'animal:FOODON_00003004',
-               'fungus:FOODON_03411261',
-               'lichen:FOODON_03412345',
-               'whole plant:PO_0000003',
-              ]
-
-ncbi_taxon = ['Actinopterygii:NCBITaxon_7898', #mix of taxon types
-              'Ecdysozoa:NCBITaxon_1206794',
-              'Echinodermata:NCBITaxon_7586',
-              'Fungi:NCBITaxon_4751',
-              'Spiralia:NCBITaxon_2697495',
-              'Viridiplantae:NCBITaxon_33090',
-              'Amphibia:NCBITaxon_8292',
-              #'Sauropsida:NCBITaxon_8457',
-              'Aves:NCBITaxon_8782',
-              'Crocodylia:NCBITaxon_1294634',
-              'Testudinata:NCBITaxon_2841271',
-              'Lepidosauria:NCBITaxon_8504',
-              #'Mammalia:NCBITaxon_40674',
-              'Artiodactyla:NCBITaxon_91561',
-              'Carnivora:NCBITaxon_33554',
-              'Chiroptera:NCBITaxon_9397',
-              'Chrysochloridae:NCBITaxon_9389',
-              'Eulipotyphla:NCBITaxon_9362',
-              'Hyracoidea:NCBITaxon_9810',
-              'Macroscelidea:NCBITaxon_28734',
-              'Metatheria:NCBITaxon_9263',
-              'Ornithorhynchidae:NCBITaxon_9256',
-              'Perissodactyla:NCBITaxon_9787',
-              'Pholidota:NCBITaxon_9971',
-              'Primates:NCBITaxon_9443',
-              'Proboscidea:NCBITaxon_9779',
-              'Rodentia:NCBITaxon_9989',
-              'Sirenia:NCBITaxon_9774',
-              'Tachyglossidae:NCBITaxon_9259',
-              'Tenrecidae:NCBITaxon_9369',
-              'Tubulidentata:NCBITaxon_9815',
-              'Xenarthra:NCBITaxon_9348',              
-             ]
-
-arg_bins = {#'fo_consumer':fo_consumer,
-            'fo_product':fo_product,
-            'fo_quality':fo_quality,
-            'fo_organism':fo_organism,
-            'ncbi_taxon':ncbi_taxon,
-           }